14-68868847-T-C

Variant names:

• chr14-68868847-T-C
• rs7401911
• ENST00000553776.1:n.447A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553776.1(BLZF2P):​n.447A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 640,220 control chromosomes in the GnomAD database, including 163,781 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.69 (36304 hom., cov: 29)
  • Exomes 𝑓: 0.72 (127477 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67
• Publications: 4 publications found

Genes affected

BLZF2P (HGNC:20049): (basic leucine zipper nuclear factor 2, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLZF2P		n.68868847T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLZF2P	ENST00000553776.1	n.447A>G		non_coding_transcript_exon_variant	Exon 3 of 4	6

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104557 AN: 151392 Hom.: 36273 Cov.: 29

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.692

GnomAD4 exome AF: 0.719 AC: 351184 AN: 488710 Hom.: 127477 Cov.: 0 AF XY: 0.719 AC XY: 194458 AN XY: 270336

African (AFR) AF: 0.696 AC: 8975 AN: 12904

American (AMR) AF: 0.815 AC: 29058 AN: 35644

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 11954 AN: 16094

East Asian (EAS) AF: 0.516 AC: 12074 AN: 23420

South Asian (SAS) AF: 0.754 AC: 48950 AN: 64948

European-Finnish (FIN) AF: 0.691 AC: 27331 AN: 39566

Middle Eastern (MID) AF: 0.704 AC: 2388 AN: 3392

European-Non Finnish (NFE) AF: 0.719 AC: 192725 AN: 268122

Other (OTH) AF: 0.720 AC: 17729 AN: 24620

GnomAD4 genome AF: 0.691 AC: 104632 AN: 151510 Hom.: 36304 Cov.: 29 AF XY: 0.691 AC XY: 51150 AN XY: 73990

African (AFR) AF: 0.677 AC: 27906 AN: 41250

American (AMR) AF: 0.770 AC: 11724 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2513 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2586 AN: 5148

South Asian (SAS) AF: 0.749 AC: 3607 AN: 4814

European-Finnish (FIN) AF: 0.665 AC: 6891 AN: 10362

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47093 AN: 67928

Other (OTH) AF: 0.696 AC: 1466 AN: 2106

Alfa AF: 0.692 Hom.: 147444

Bravo AF: 0.695

Asia WGS AF: 0.703 AC: 2442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.6
DANN	Benign	0.55
PhyloP100		2.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7401911; hg19: chr14-69335564;